Working with Horvath Mammal (Mammal40) Array

SeSAMe supports Mammal 40 array natively.

Load Mammal40 array IDAT

res_grn = sesameDataDownload("GSM4411982_Grn.idat.gz")
res_red = sesameDataDownload("GSM4411982_Red.idat.gz")
sset = readIDATpair(sprintf("%s/GSM4411982", res_red$dest_dir))

## Warning in ExperimentHub(localHub = TRUE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
##   Problematic cache: /home/kabilan/.cache/ExperimentHub
##   See ExperimentHub vignette section on 'Default Caching Location Update'

## Warning in ExperimentHub(localHub = FALSE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
##   Problematic cache: /home/kabilan/.cache/ExperimentHub
##   See ExperimentHub vignette section on 'Default Caching Location Update'

## Warning in ExperimentHub(localHub = TRUE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
##   Problematic cache: /home/kabilan/.cache/ExperimentHub
##   See ExperimentHub vignette section on 'Default Caching Location Update'

Preprocess the sigset to produce beta values. The standard noob, dyeBiasCorrTypeINorm works as expected:

sset_normalized = sset %>%
                  noob %>%
                  dyeBiasCorrTypeINorm

Retrieve beta values using the following commands

betas = sset_normalized %>%
        qualityMask %>%
        detectionMask %>%
        getBetas